Despite the conventional wisdom, converting to innodb_file_per_table will not necessarily help you. It depends on your situation. If most of your growth is in a single table, you will only have transferred the problem from the ibdata1 file to a new file. The ibdata1 file may also continue to grow, since innodb uses it for several kinds of temporary storage such as the insert buffer and the undo logs (AKA "rollback segment").
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